Merge branch 'release-0.7.0' into 'master'

Release 0.7.0



See merge request !449

.gitignore

@@ -10,7 +10,5 @@ git.properties
 .idea/*
 *.iml
 target/
-public/target/
-protected/target/
 site/
 *.sc
\ No newline at end of file

README.md

@@ -55,18 +55,18 @@ At the moment, we do not provide links to download the Biopet package. If you ar
 
 ## Contributing to Biopet
 
-Biopet is based on the Queue framework developed by the Broad Institute as part of their Genome Analysis Toolkit (GATK) framework. The current Biopet release is based on the GATK 3.4 release.
+Biopet is based on the Queue framework developed by the Broad Institute as part of their Genome Analysis Toolkit (GATK) framework. The current Biopet release is based on the GATK 3.5 release.
 
 We welcome any kind of contribution, be it merge requests on the code base, documentation updates, or any kinds of other fixes! The main language we use is Scala, though the repository also contains a small bit of Python and R. Our main code repository is located at [https://github.com/biopet/biopet](https://github.com/biopet/biopet/issues), along with our issue tracker.
 
 ## Local development setup
 
-To develop Biopet, Java 7, Maven 3.2.2, and GATK Queue 3.4 is required. Please consult the Java homepage and Maven homepage for the respective installation instruction. After you have both Java and Maven installed, you would then need to install GATK Queue. However, as the GATK Queue package is not yet available as an artifact in Maven Central, you will need to download, compile, and install GATK Queue first.
+To develop Biopet, Java 7, Maven 3.3.3, and GATK Queue 3.5 is required. Please consult the Java homepage and Maven homepage for the respective installation instruction. After you have both Java and Maven installed, you would then need to install GATK Queue. However, as the GATK Queue package is not yet available as an artifact in Maven Central, you will need to download, compile, and install GATK Queue first.
 
 ~~~
 $ git clone https://github.com/broadgsa/gatk-protected
-$ cd gatk-protected
-$ git checkout 3.4                              # the current release is based on GATK 3.4
+$ cd gatk
+$ git checkout 3.5                              # the current release is based on GATK 3.5
 $ mvn -U clean install
 ~~~
 

bam2wig/pom.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+    Biopet is built on top of GATK Queue for building bioinformatic
+    pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+    SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+    should also be able to execute Biopet tools and pipelines.
+
+    Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+
+    Contact us at: sasc@lumc.nl
+
+    A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
+    license; For commercial users or users who do not want to follow the AGPL
+    license, please contact us to obtain a separate license.
+
+-->
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+    <modelVersion>4.0.0</modelVersion>
+
+    <artifactId>Bam2Wig</artifactId>
+    <packaging>jar</packaging>
+
+    <parent>
+        <groupId>nl.lumc.sasc</groupId>
+        <artifactId>Biopet</artifactId>
+        <version>0.7.0</version>
+        <relativePath>../</relativePath>
+    </parent>
+
+    <inceptionYear>2014</inceptionYear>
+    <name>Bam2Wig</name>
+
+    <dependencies>
+        <dependency>
+            <groupId>nl.lumc.sasc</groupId>
+            <artifactId>BiopetCore</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>nl.lumc.sasc</groupId>
+            <artifactId>BiopetExtensions</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>org.scalatest</groupId>
+            <artifactId>scalatest_2.10</artifactId>
+            <version>2.2.1</version>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.testng</groupId>
+            <artifactId>testng</artifactId>
+            <version>6.8</version>
+            <scope>test</scope>
+        </dependency>
+    </dependencies>
+
+</project>
\ No newline at end of file

bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala

+/**
+ * Biopet is built on top of GATK Queue for building bioinformatic
+ * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+ * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+ * should also be able to execute Biopet tools and pipelines.
+ *
+ * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+ *
+ * Contact us at: sasc@lumc.nl
+ *
+ * A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
+ * license; For commercial users or users who do not want to follow the AGPL
+ * license, please contact us to obtain a separate license.
+ */
+package nl.lumc.sasc.biopet.pipelines.bamtobigwig
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
+import nl.lumc.sasc.biopet.extensions.WigToBigWig
+import nl.lumc.sasc.biopet.extensions.igvtools.IGVToolsCount
+import org.broadinstitute.gatk.queue.QScript
+
+/**
+ * Pipeline to create BigWigle files from a bam file
+ *
+ * Created by pjvan_thof on 1/29/15.
+ */
+class Bam2Wig(val root: Configurable) extends QScript with BiopetQScript {
+  def this() = this(null)
+
+  @Input(doc = "Input bam file", required = true)
+  var bamFile: File = null
+
+  def init(): Unit = {
+    inputFiles :+= new InputFile(bamFile)
+  }
+
+  def outputWigleFile = new File(outputDir, bamFile.getName + ".wig")
+  def outputTdfFile = new File(outputDir, bamFile.getName + ".tdf")
+  def outputBwFile = new File(outputDir, bamFile.getName + ".bw")
+
+  def biopetScript(): Unit = {
+    val bs = new BamToChromSizes(this)
+    bs.bamFile = bamFile
+    bs.chromSizesFile = bamFile.getAbsoluteFile + ".chrom.sizes"
+    bs.isIntermediate = true
+    add(bs)
+
+    val igvCount = new IGVToolsCount(this)
+    igvCount.input = bamFile
+    igvCount.genomeChromSizes = bs.chromSizesFile
+    igvCount.wig = Some(outputWigleFile)
+    igvCount.tdf = Some(outputTdfFile)
+    add(igvCount)
+
+    val wigToBigWig = new WigToBigWig(this)
+    wigToBigWig.inputWigFile = igvCount.wig.get
+    wigToBigWig.inputChromSizesFile = bs.chromSizesFile
+    wigToBigWig.outputBigWig = outputBwFile
+    add(wigToBigWig)
+  }
+}
+
+object Bam2Wig extends PipelineCommand {
+  def apply(root: Configurable, bamFile: File): Bam2Wig = {
+    val bamToBigWig = new Bam2Wig(root)
+    bamToBigWig.outputDir = bamFile.getParentFile
+    bamToBigWig.bamFile = bamFile
+    bamToBigWig.init()
+    bamToBigWig.biopetScript()
+    bamToBigWig
+  }
+}
\ No newline at end of file

bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToChromSizes.scala

+/**